Now that the elucidation of the gene arrangement of humans has been substantially completed, many researchers have focused on a molecule having the ability to specifically bind to a particular base sequence. Non-Patent Document 1 and the like show that Dervan et al. found that an antiparallel oriented “N-methylpyrrole”-“N-methylimidazole” polyamide (hereinafter, N-methylpyrrole being simply referred to as “pyrrole” or “Py”; and N-methylimidazole being simply referred to as “imidazole” or “Im”) base-sequence-specifically binds to the minor groove of DNA. Furthermore, general rules that Py-Im recognizes a C-G base pair, Im-Py recognizes a G-C base pair, and Py-Py recognizes an A-T base pair or a T-A base pair have been derived.
Various hairpin polyamides and cyclic polyamides have been synthesized by introducing a covalent bond into Py-Im in order to prevent the loss of entropy due to binding and to achieve stronger binding and the ability to recognize a sequence. A β-linker (—NHCH2CH2CO—) and a γ-linker (—NHCH2CH2CH2CO—) are typically known. It has been described that a hairpin polyamide containing the γ-linker (—NHCH2CH2CH2CO—) particularly has excellent binding ability and recognition ability. In addition, the structure of a complex between the hairpin polyamide containing the γ-linker and DNA has been determined (see Non-Patent Document 2). β-β recognizes an A-T base pair or a T-A base pair. Similarly, the γ-linker recognizes an A-T base pair or a T-A base pair. The γ-linker has a γ-turn structure represented by the trifurcate portion of a bent hairpin model.
These molecules each have an association constant and specificity comparable to a transcription factor and the like. However, the regulation of gene expression is performed by inhibiting binding of the transcription factor. Thus, base sequences that can be targeted is significantly limited (for example, see Non-Patent Document 3).
The inventors have developed a hybrid molecule of a Py-Im polyamide bound to a segment A (Du) serving as an alkylating moiety of duocarmycin A, which is an antibiotic, and filed an application (for example, Patent Document 1). The hybrid molecule selectively alkylated one site of a DNA fragment of 450 base pairs on the basis of the sequence recognition ability of the Py-Im polyamide (for example, see Non-Patent Document 4). However, completion of the reaction requires several days. Furthermore, the reaction efficiency was as low as several percent.
In contrast, the inventors found that ImPyLDu86 containing a vinyl linker (L) disposed between a functional group (hereinafter, referred to as an “alkylating moiety”) for alkylating DNA and the Py-Im polyamide dimerizes and selectively reacts with both chains at sites thereof located 5 base pairs apart in a 5′-YG(A/T)CR-3′ sequence (wherein Y represents a pyrimidine base; and R represents a purine base) at a low concentration to cause alkylation with an efficiency as high as 70%. That is, the inventors found considerable improvement in reactivity and efficiency by introducing the linker moiety (for example, see Non-Patent Document 5).
Patent Document 1: International Publication No. WO00/15641
Non-Patent Document 1: J. Am. Chem. Soc. 1997, 119, 7636
Non-Patent Document 2: J. Am. Chem. Soc. 1997, 119, 7909
Non-Patent Document 3: J. Am. Chem. Soc. 2000, 122, 4856
Non-Patent Document 4: J. Am. Chem. Soc. 1999, 121, 4961
Non-Patent Document 5: J. Am. Chem. Soc. 2000, 122, 1602